| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Ablikim, M., et al.
(author)
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Observation of the decay psi(3686) -> Lambda(Sigma)over-bar(+/-) pi(-/+) + c.c
- 2013
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112007-
-
Journal article (peer-reviewed)abstract
- Using a sample of 1:06 X 10(8) psi(3686) events collected with the BESIII detector, we present the first observation of the decays of psi(3686) -> Lambda(Sigma) over bar (+) pi(-) + c.c. and psi(3686) -> Lambda(Sigma) over bar (-) pi(+) + c.c. The branching fractions are measured to be B(psi(3686) -> Lambda(Sigma) over bar (+) pi(-) + c.c.) = (1.40 +/- 0.03 +/- 0.13) X 10(-4) and B(psi(3686) -> Lambda (Sigma) over bar (-) pi(+) + c.c.) = (1.54 +/- 0.04 +/- 0.13) X 10(-4) where the first errors are statistical and the second ones systematic.
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| 4. |
- Ablikim, M., et al.
(author)
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Search for eta(c)(2S)h(c) -> p(p)over-bar decays and measurements of the chi(cJ) -> p(p)over-bar branching fractions
- 2013
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112001-
-
Journal article (peer-reviewed)abstract
- Using a sample of 1.06 x 10(8)psi(3686) events collected with the BESIII detector at BEPCII, the decays eta(c)(2S) -> p (p) over bar and h(c) -> p (p) over bar are searched for, where eta(c)(2S) and h(c) are reconstructed in the decay chains psi(3686) -> gamma eta(c)(2S), eta(c)(2S) -> p (p) over bar and psi(3686) -> pi(0)h(c), h(c) -> p (p) over bar, respectively. No significant signals are observed. The upper limits of the product branching fractions are determined to be B(psi(3686) -> gamma eta(c)(2S)) x B(eta(c)(2S) -> p (p) over bar) < 1.4 x 10(-6) and B(psi(3686) -> pi(0)h(c)) x B(h(c) -> p<(p)over bar>) < 1.3 x 10(-7) at the 90% C.L.. The branching fractions for chi(cJ) -> p<(p)over bar> (J = 0, 1, 2) are also measured to be (24.5 +/- 0.8 +/- 1.3, 8.6 +/- 0.5 +/- 0.5, 8.4 +/- 0.5 +/- 0.5) x 10(-5), which are the world's most precise measurements.
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| 5. |
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- 2019
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Journal article (peer-reviewed)
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| 6. |
- Pecunia, Vincenzo, et al.
(author)
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Roadmap on energy harvesting materials
- 2023
-
In: Journal of Physics. - : IOP Publishing. - 2515-7639. ; 6:4
-
Journal article (peer-reviewed)abstract
- Ambient energy harvesting has great potential to contribute to sustainable development and address growing environmental challenges. Converting waste energy from energy-intensive processes and systems (e.g. combustion engines and furnaces) is crucial to reducing their environmental impact and achieving net-zero emissions. Compact energy harvesters will also be key to powering the exponentially growing smart devices ecosystem that is part of the Internet of Things, thus enabling futuristic applications that can improve our quality of life (e.g. smart homes, smart cities, smart manufacturing, and smart healthcare). To achieve these goals, innovative materials are needed to efficiently convert ambient energy into electricity through various physical mechanisms, such as the photovoltaic effect, thermoelectricity, piezoelectricity, triboelectricity, and radiofrequency wireless power transfer. By bringing together the perspectives of experts in various types of energy harvesting materials, this Roadmap provides extensive insights into recent advances and present challenges in the field. Additionally, the Roadmap analyses the key performance metrics of these technologies in relation to their ultimate energy conversion limits. Building on these insights, the Roadmap outlines promising directions for future research to fully harness the potential of energy harvesting materials for green energy anytime, anywhere.
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| 7. |
- Wang, Wen‐Bo, et al.
(author)
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Chromosome‐scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata
- 2023
-
In: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 238:5, s. 2016-2032
-
Journal article (peer-reviewed)abstract
- Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated.First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation.Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays.Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.
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| 8. |
- Cheng, Shi-Ping, et al.
(author)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
-
Journal article (peer-reviewed)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 9. |
- Ding, Yun Mei, et al.
(author)
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Effect of social support on illness perception in patients with atrial fibrillation during “Blanking Period” : Mediating role of sense of mastery
- 2023
-
In: Nursing Open. - : Wiley. - 2054-1058. ; 10:1, s. 115-122
-
Journal article (peer-reviewed)abstract
- Aim: To explore whether sense of mastery can mediate the relationship between social support and illness perception in patients with atrial fibrillation (AF) who were at the “Blanking Period.”. Design: A cross-sectional design. Methods: 405 patients with AF who were at the “Blanking Period” in the Affiliated Hospital of Qingdao University were recruited; they completed a set of questionnaires, including the Perceived Social Support Scale, the Personal Mastery Scale and the Brief Illness Perception Questionnaire. Results: Social support and sense of mastery were both adversely connected to illness perception. The indirect effect of social support on illness perception through sense of mastery was negative, accounting for 86.04% of the total effect. Conclusion: During the “Blanking Period,” better social support and sense of mastery contribute to a positive illness perception of AF patients. Social support also can influence patients' illness perception indirectly via the mediator of sense of mastery.
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| 10. |
- Guo, Jing-Fang, et al.
(author)
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Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana
- 2023
-
In: Journal of Systematics and Evolution. - : John Wiley & Sons. - 1674-4918 .- 1759-6831. ; 61:1, s. 143-156
-
Journal article (peer-reviewed)abstract
- Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.
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| 11. |
- Liang, Jiamin, et al.
(author)
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A phylogenetic framework of Palaearctic and Indomalayan Limacodidae (Lepidoptera, Zygaenoidea) based on sequence capture data
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In: Systematic Entomology. - 0307-6970.
-
Journal article (peer-reviewed)abstract
- The slug moth family Limacodidae is a cosmopolitan group of economic importance, but its higher level systematics remains poorly understood. Here, we present a robust, higher level phylogenetic framework for Palaearctic and Indomalayan members of the family using sequence capture data of 148 nuclear protein-coding and 13 mitochondrial markers from 145 samples of 126 species in 67 genera representing all five morphologically delineated limacodid lineages. Our results strongly support the monophyly of Limacodidae in which six major clades are recognized. The relationships among these clades are revealed, with Phrixolepia-clade being the most basal group followed by Apoda-clade, Euphlyctinides-clade, Cania-clade and Phlossa-clade + Parasa-clade, respectively. We also add publicly available DNA barcode sequences from additional species worldwide to this phylogenetic framework to infer the most completely sampled phylogeny of Limacodidae to date. Our work provides a major step towards understanding the systematics and evolution of slug moths.
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| 12. |
- Wang, Chaoqian, et al.
(author)
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A stepwise microwave synergistic pyrolysis approach to produce sludge-based biochars : Feasibility study simulated by laboratory experiments
- 2020
-
In: Fuel. - : Elsevier. - 0016-2361 .- 1873-7153. ; 272, s. 1-10
-
Journal article (peer-reviewed)abstract
- A stepwise microwave synergistic pyrolysis (SMSP) approach is proposed as a new way to relieve disposal problems of the sewage sludge. Here the sludge is first pre-pyrolyzed by a conventional heating stage, and then rapidly pyrolyzed by a microwave-induced heating stage without any extra microwave absorbers or blending needed. Under simulated process pyrolysis conditions, the dried sludge, intermediate and final sludge-based biochar samples were prepared in the laboratory. Their chemical composition, microstructure and morphology, and leaching toxicity of heavy metals were carefully characterized and analyzed by various techniques such as proximate and ultimate analysis, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, Brunauer-Emmett-Teller (BET), and scanning electron microscope equipped with energy-dispersive x-ray spectroscopy (SEM-EDX). Results showed that the pre-pyrolytic biochar can be rapidly heated up to 1100 °C within 5 min under microwave irradiation. The pre-pyrolytic stage increased the carbonization and ash enrichment degree of the sludge which itself acted as a good microwave absorber while achieving a quick temperature rise under microwave irradiation. The ash remaining ratio and the specific surface area of the biochar derived from the SMSP approach (labelled as SBC2) are increased by 6.46% and 16.17% respectively, compared with the conventional biochar sample (SBC1). And SBC2 still had diverse surface functional groups kept after SMSP. The residual ratios of Ni, Cu, Zn, Pb, Cr and Cd in SBC2 was more noticeable than in SBC1 but the leaching ratios quite the contrary. Vitrification is also well proved by the increment of quartz peak detected by XRD tests, and the formation of melted glassy spheres with elemental composition of Si, Ca, Al observed by SEM-EDX. It can favorably increase solidification level and decrease leaching toxicity of heavy metals in the SBC2. The feasibility of this proposed SMSP concept has been positively supported by our experimental results. The properties of the sludge-based biochar produced from the SMSP approach also show great potential to be utilized as precursors to produce various adsorbents.
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| 13. |
- Yang, Fu-Sheng, et al.
(author)
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Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- 2020
-
In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
-
Journal article (peer-reviewed)abstract
- Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
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| 14. |
- Zhang, Huai, et al.
(author)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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In: Hepatology international. - 1936-0541.
-
Journal article (peer-reviewed)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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| 15. |
- Blanton, Michael R., et al.
(author)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
-
In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Journal article (peer-reviewed)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 16. |
- Chen, Ziqing, et al.
(author)
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Phosphodiesterase 4A confers resistance to PGE2-mediated suppression in CD25(+)/CD54(+) NK cells
- 2021
-
In: EMBO Reports. - : EMBO Press. - 1469-221X .- 1469-3178. ; 22:3
-
Journal article (peer-reviewed)abstract
- Inadequate persistence of tumor-infiltrating natural killer (NK) cells is associated with poor prognosis in cancer patients. The solid tumor microenvironment is characterized by the presence of immunosuppressive factors, including prostaglandin E2 (PGE2), that limit NK cell persistence. Here, we investigate if the modulation of the cytokine environment in lung cancer with IL-2 or IL-15 renders NK cells resistant to suppression by PGE2. Analyzing Cancer Genome Atlas (TCGA) data, we found that high NK cell gene signatures correlate with significantly improved overall survival in patients with high levels of the prostaglandin E synthase (PTGES). In vitro, IL-15, in contrast to IL-2, enriches for CD25(+)/CD54(+) NK cells with superior mTOR activity and increased expression of the cAMP hydrolyzing enzyme phosphodiesterase 4A (PDE4A). Consequently, this distinct population of NK cells maintains their function in the presence of PGE2 and shows an increased ability to infiltrate lung adenocarcinoma tumors in vitro and in vivo. Thus, strategies to enrich CD25(+)/CD54(+) NK cells for adoptive cell therapy should be considered.
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| 17. |
- Guo, Jing-Fang, et al.
(author)
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Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau
- 2023
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In: Plant Communications. - : Cell Press. - 2590-3462. ; 4:4
-
Journal article (peer-reviewed)abstract
- Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.
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| 18. |
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| 19. |
- Jia, Kai-Hua, et al.
(author)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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In: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
-
Journal article (peer-reviewed)abstract
- Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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| 20. |
- Liu, Shuyu, et al.
(author)
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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
- 2022
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In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Journal article (peer-reviewed)abstract
- Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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| 21. |
- Shi, Tian-Le, et al.
(author)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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In: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
-
Journal article (peer-reviewed)abstract
- Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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| 22. |
- Zhang, Wei, et al.
(author)
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Tannic acid-mediated dual peptide-functionalized scaffolds to direct stem cell behavior and osteochondral regeneration
- 2020
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In: Chemical Engineering Journal. - : Elsevier. - 1385-8947 .- 1873-3212. ; 396
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Journal article (peer-reviewed)abstract
- The development of cell-instructive scaffolds, which provide biochemical cues to direct endogenous bone marrow-derived mesenchymal stem cells (BMSCs) behavior, has the potential to revolutionize osteochondral tissue engineering. However, scaffold material itself is generally lacking the inductive signals. Here, a novel peptide-functionalized scaffold was prepared by prime-coating Ca-alginate scaffold with tannic acid (TA) followed by conjugation of E7/P15 peptides (CA-TA-E7/P15). The system leveraged TA as a reactive intermediate between Ca-alginate and peptides due to the multiple functional groups of TA. These interactions induced by TA prime-coating contributed to enhanced scaffold stability and mechanical properties, increased peptide conjugation and sustained release of peptides without affecting their bioactivity, in a TA concentration-dependent manner. The conjugation of E7/P15 peptides endowed the scaffold with the potential to enhance BMSCs recruitment and deposition of cartilage and bone extracellular matrix (ECM). Furthermore, the prepared CA-TA-E7/P15 scaffold showed a promoted biological performance of simultaneous cartilage and subchondral bone regeneration in rabbit osteochondral defect model. These findings indicate that TA is an effective surface modification intermediate and crosslinking aid, and that the CA-TA-E7/P15 scaffold developed in this study serves as a promising cell-instructive scaffold for osteochondral regeneration.
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| 23. |
- Zhang, Xiaoyu, et al.
(author)
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Comparative Study on Pyrido[3,4-b]pyrazine-Based Sensitizers by Tuning Bulky Donors for Dye-Sensitized Solar Cells
- 2015
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In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 7:4, s. 2760-2771
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Journal article (peer-reviewed)abstract
- Dye-sensitized solar cells (DSSCs) with cobalt electrolytes have gained increasing attention. In this Research Article, two new pyrido[3,4-b]pyrazine-based sensitizers with different cores of bulky donors (indoline for DT-1 and triphenylamine for DT-2) were designed and synthesized for a comparative study of their photophysical and electrochemical properties and device performance and were also analyzed through density functional theory calculations. The results of density function theory calculations reveal the limited electronic communication between the biphenyl branch at the cis-position of N-phenylindoline and the indoline core, which could act as an insulating blocking group and inhibit the dye aggregation and charge recombination at the interface of TiO2/dye/electrolyte. As expected, DSSCs based on DT-1 with cobalt redox electrolyte gained a higher photoelectric conversion efficiency of 8.57% under standard AM 1.5 G simulated sunlight, with J(sc) = 16.08 mA cm(-2), V-oc = 802 mV, and FF = 0.66. Both electrochemical impedance spectroscopy (EIS) and intensity-modulated photovoltage spectroscopy (IMVS) suggest that charge recombination in DSSCs based on DT-1 is much less than that in their counterparts of DT-2, owing to the bigger donor size and the insulating blocking branch in the donor of DT-1.
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| 24. |
- Zhang, Xiaorong, et al.
(author)
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Review of chemical looping process for carbonaceous feedstock Conversion : Rational design of oxygen carriers
- 2022
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In: Fuel. - : Elsevier. - 0016-2361 .- 1873-7153. ; 325
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Research review (peer-reviewed)abstract
- The chemical looping partial oxidation (CLPO) process as a technology of chemical looping process (CLP) is recognized as a potential strategy for the efficient and clean conversion of fuels into syngas/H2. Herein, in view of the importance of low-cost high-performance metal oxides as oxygen carriers (OCs) for this conversion, we systematically review the classification and CLPO applications of such OCs and discuss the improvement of OC reactivity and stability via the creation of metal–metal or metal–support synergism, the generation of oxygen vacancies, and the enhancement of deactivation resistance. Further, we present the results of theoretical and experimental characterizations probing ion diffusion and surface reactions to provide insights into the related reaction mechanisms and touch on the challenges and opportunities of developing metal oxides with excellent reactivity and long-term cycling stability in CLP. Thus, this review facilitates the design and performance regulation of OCs for future energy conversion systems.
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